Reproducible Manuscripts

Introduction

Why This Workshop?

From Journal Articles…

…To Research Compendiums.

More Specifically…

We want Dynamic Document Generation, where we can:

  • combine narrative with code

  • automatically generate figures and tables

  • automatically render results in text

  • format the content into a scientific paper (including citations!)

  • rinse & repeat

Advantages

  • One major benefit is the elimination of human error in copying and pasting results, as automated methods can update results, figures, and tables with major revisions.

Using an automated method for scraping APA-formatted stats out of PDFs, Nuijten et al. (⊕2016) found that over 10% of p-values in published papers were inconsistent with the reported details of the statistical test, and 1.6% were what they called “grossly” inconsistent, e.g. difference between the p-value and the test statistic meant that one implied statistical significance and the other did not. Nearly half of all papers had errors in them.

Advantages

  • The use of reproducible documents also allows for easy revisions and specification of desired figures and tables.

When revisions are requested, one might have to tweak tables and figures by hand constantly, leading to a major incentive never to rerun analyses because it would mean re-pasting and re-illustratoring all the numbers and figures in a paper.

Advantages

  • Furthermore, computational reproducibility is promoted, which allows others to easily verify and replicate research findings.

While programming environments may seem counter-intuitive for writing papers, they ultimately prevent mistakes and save time.

How Do We Pull This off?

Enter Quarto…

  • Quarto® is an open-source scientific and technical publishing system built on Pandoc.

  • It’s the ‘new generation’ of R Markdown, designed to work multiple programming languages + tools in an aligned way.

  • Quarto can weave together narrative text and code to produce elegantly formatted output as documents, web pages, blog posts, books and more.

Let’s Get Started!

Your Turn!

  • Go to the Getting Started chapter of the workshop book and follow the instructions for your programming language.
10:00

Output

Anatomy of a Quarto Document

  • Metadata & Header (YAML)
---
format: html
---
  • Code
```{r}
#| eval: true
library(dplyr)
mtcars %>% 
  group_by(cyl) %>%
  summarize(mean = mean(mpg), .groups = "drop")
```
# A tibble: 3 × 2
    cyl  mean
  <dbl> <dbl>
1     4  26.7
2     6  19.7
3     8  15.1
  • Text
# Heading 1
This is a sentence with some **bold text**, some *italic text* and an [image](image.png).